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Chapter 4 (part 1) protein structure introduction- 2nd structure
Chapter 4 covers protein structure and function, detailing terminology such as conformation and protein classification into simple, conjugated, monomeric, and multimeric categories. It discusses the four levels of protein structure and the significance of non-covalent forces in determining that structure, as well as common secondary structures like alpha helices and beta-sheets. The chapter highlights various protein functions, including catalysis, transport, and structural roles, while addressing the impact of amino acid changes on protein functionality, exemplified by conditions like sickle cell anemia and osteoarthritis.
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Chapter 4 (part 1) protein structure introduction- 2nd structure
- 1. Chapter 4 Protein3-Dimensional Structure and Function
- 2. Terminology • Conformation– spatial arrangement of atoms in a protein • Native conformation – conformation of functional protein
- 6. Protein Classification •Simple – composed only of amino acid residues • Conjugated – contain prosthetic groups (metal ions, co-factors, lipids, carbohydrates) Example: Hemoglobin – Heme
- 7. Protein Classification •One polypeptide chain - monomeric protein • More than one - multimeric protein • Homomultimer - one kind of chain • Heteromultimer - two or more different chains (e.g. Hemoglobin is a heterotetramer. It has two alpha chains and two beta chains.)
- 8. Protein Classification Fibrous– 1) polypeptides arranged in long strands or sheets 2) water insoluble (lots of hydrophobic AA’s) 3) strong but flexible 4) Structural (keratin, collagen) Globular – 1) polypeptide chains folded into spherical or globular form 2) water soluble 3) contain several types of secondary structure 4) diverse functions (enzymes, regulatory proteins)
- 9.
- 10. Protein Function •Catalysis – enzymes • Structural – keratin • Transport – hemoglobin • Trans-membrane transport – Na+/K+ ATPases • Toxins – rattle snake venom, ricin • Contractile function – actin, myosin • Hormones – insulin • Storage Proteins – seeds and eggs • Defensive proteins – antibodies
- 11. 4 Levels ofProtein Structure
- 12. Non-covalent forces importantin determining protein structure • van der Waals: 0.4 - 4 kJ/mol • hydrogen bonds: 12-30 kJ/mol • ionic bonds: 20 kJ/mol • hydrophobic interactions: <40 kJ/mol
- 13. 1o Structure Determines2o, 3o, 4o Structure • Sickle Cell Anemia – single amino acid change in hemoglobin related to disease • Osteoarthritis – single amino acid change in collagen protein causes joint damage
- 14. Classes of 2oStructure • Alpha helix • B-sheet • Loops and turns
- 15. 2o Structure Relatedto Peptide Backbone •Double bond nature of peptide bond cause planar geometry •Free rotation at N - aC and aC-carbonyl C bonds •Angle about the C(alpha)-N bond is denoted phi (f) •Angle about the C(alpha)-C bond is denoted psi (y) •The entire path of the peptide backbone is known if all phi and psi angles are specified
- 16. Not all f/yangles are possible
- 17. Ramachandran Plots •Describesacceptable f/y angles for individual AA’s in a polypeptide chain. •Helps determine what types of 2o structure are present
- 18. Alpha-Helix • Firstproposed by Linus Pauling and Robert Corey in 1951 • Identified in keratin by Max Perutz • A ubiquitous component of proteins • Stabilized by H-bonds
- 19. Alpha-Helix •Residues per turn: 3.6 •Rise per residue: 1.5 Angstroms •Rise per turn (pitch): 3.6 x 1.5A = 5.4 Angstroms •amino hydrogen H-bonds with carbonyl oxygen located 4 AA’s away forms 13 atom loop Right handed helix
- 20. Alpha-Helix All H-bondsin the alpha-helix are oriented in the same direction giving the helix a dipole with the N-terminus being positive and the C-terminus being negative
- 21. Alpha-Helix •Side chaingroups point outwards from the helix •AA’s with bulky side chains less common in alpha-helix •Glycine and proline destabilizes alpha-helix
- 22. Amphipathic Alpha-Helices + One side of the helix (dark) has mostly hydrophobic AA’s Two amphipathic helices can associate through hydrophobic interactions
- 23. Beta-Strands and Beta-Sheets • Also first postulated by Pauling and Corey, 1951 • Strands may be parallel or antiparallel • Rise per residue: • – 3.47 Angstroms for antiparallel strands – 3.25 Angstroms for parallel strands – Each strand of a beta sheet may be pictured as a helix with two residues per turn
- 24. Beta-Sheets • Beta-sheetsformed from multiple side-by-side beta-strands. • Can be in parallel or anti-parallel configuration • Anti-parallel beta-sheets more stable
- 25. Beta-Sheets • Sidechains point alternately above and below the plane of the beta-sheet • 2- to 15 beta-strands/beta-sheet • Each strand made of ~ 6 amino acids
- 26. Loops and turns Loops • Loops usually contain hydrophillic residues. • Found on surfaces of proteins • Connect alpha-helices and beta-sheets Turns • Loops with < 5 AA’s are called turns • Beta-turns are common
- 27. Beta-turns • allowsthe peptide chain to reverse direction • carbonyl C of one residue is H-bonded to the amide proton of a residue three residues away • proline and glycine are prevalent in beta turns